I didn't grew up with English-language, that's why it is sometimes a bit confusing, especially after a normal working day, when I am a bit tired... Dear Duolingo think about teaching Hungarian for Germanspeakings!!! Yes or yes? ;))

It initially sounded a little odd to me, but you would hear it in American English. It sounds less "odd" if you say "What basket is the apple in?", "What room is the apple in?"......."In what is the apple?" is even more peculiar. (You could however insert a poetic pause between -what- and -is- to dramatically improve the syntax) This sentence also works with, "In what basket is the apple?", "In what room is the apple?"......

Yes - "what is the apple in" is normal, spoken English. There was a movement to have English match Latin grammar but this is pretty much discredited and even the Oxford English Grammar considers a deferred preposition the natural choice in many cases.